rs4088473

Positions:

• chr11-63411679-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.435 in 151,944 control chromosomes in the GnomAD database, including 16,690 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (16690 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65963 AN: 151826 Hom.: 16649 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.435

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.435 AC: 66077 AN: 151944 Hom.: 16690 Cov.: 31 AF XY: 0.436 AC XY: 32417 AN XY: 74274

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.439

Alfa AF: 0.358 Hom.: 1441

Bravo AF: 0.461

Asia WGS AF: 0.653 AC: 2248 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.035
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4088473; hg19: chr11-63179151;